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For newer laptops, there is a safe sleep mode that writes the entire contents of RAM to a file called sleepimage that is located in /private/var/vm. My laptop has 3 GB RAM so this file is 3 GB in size. This file, like the swap files in the same directory, doesn't seem to be copied by SuperDuper (copying them would serve no purpose).
In my case, the swap files had grown to take up about 1 GB and with the 3 GB sleepfile, I saw a ~ 4 GB difference between the clone and the original drive artificially caused by these temporary files that would serve no purpose had they been copied.
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